The union said workers would be asked if they want to strike or take action short of a strike on Monday and that its ballot would run for three weeks.
It warned action could cost AWE millions of pounds at a time when the government has said it will invest £15bn in a new nuclear programme.
Prospect accused AWE of “drip-feeding” information over weeks so full consultation with staff was “impossible”.
The union’s general secretary Mike Clancy said: “There are few more skilled and qualified people in the UK than the nuclear specialists at AWE, they deserve to be treated with significantly more respect by their employer and not subjected to shambolic processes such as this reorganisation.
“If AWE do not agree to our reasonable asks then we will have no choice but to proceed with industrial action.”
But the MoD spokesperson said AWE’s workforce was being “reshaped to deliver on the government’s commitment to the nuclear deterrent, refocussing resources to build capability rather than reducing headcount”.
“We are aware of Prospect’s intention to ballot its members,” they said.
“While this is disappointing, we respect the lawful right to ballot. AWE is committed to constructive dialogue and meaningful consultation on the issues raised.
“In the event of industrial action, pre-planned contingency measures will be implemented to maintain defence outputs and the safety and security of AWE’s sites.”